RetrogeneDB ID: retro_tbel_4448

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_83836:2..1025(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CDYL2
• Ensembl ID: ENSTBEG00000000034
• Aliases: None
• Description: chromodomain protein, Y-like 2 [Source:HGNC Symbol;Acc:23030]

Sequence

>retro_tbel_4448
ATTGAAAAGATTGTAGACAAGAGAAAAAATTTTAAAAAAAAATGAAAGTATCTTACCCGGTGGAAAGGCTATGGGAGCAC
AGAGGACACGTGGGAGCCAGAACACCACCTCTTGCACTGTGAGGAGTTTATCGACTAGTTCCATGGGCTGCACGTATCCA
AGGACAAGAGGATCAGGCCAGGGAAACAGTCTAACACCTCCAAGCTCCTACGTGACAGCCGGAGCTCACCGAGTGAAAAA
CTAGCCCATAGACCTTCAGAACCTGGGAAGAGCAAAGGGACTTCCCATAAATGGAAGTGCATCAACCCTCCCCTATCTAA
GCGGAAGAAGGGGTACTCCAGCAAGCCCCCTGCAGGGGGCAATCGAGCTGCCAAGATGGTGTCTTACAGGACTACCCCCA
GCGGTTTGAAAATAATGCCCCTGAAAAAGGCTCAGAATGGGATGGAAAATAGGGACACCGGCTCTGAGAAGGACGAGAGG
CACTTTGGAAATGGGTCACATCAGCCTGGCTTGGACTTGAAGGATCATGTTGGAGAGCAGGATGTGGATGATTGTGAAGT
GAACCATGCAGCACTGGCAGAGAACGGGCTCGGCTCTGCTCTGACTAATGGGGTATTGAACTTCCACAGCCCTGCAAAGA
GAAAGCTGGAAACAGAAAAGGACTATGTCTTTGACAAGAGGCTCAGGTACAGCATCTGCCAGAATGAAAGCAACTGTCGG
TTTCAAAATATTGTCGTGCAGAAAGAAGAAGGGGTCACACACATCTTGCTGTCCAGCCAGACCTCGGATAACAACGCACT
GACACCTGAGATCATGAAGGAAGTCCGGCGAGCACTCTGCAACGCAGCCACAGATGACAGCAAACTGTTGCTCTTCAGTG
CAGTGGGGACTGTGTTCTGGAGTGGCCTAGATTACTCCAACCTAATTGGTCAGTTGTCCAGTGACCGAAGAAAGGAGAGC
ACTCGGATTGCCGAAGCCATCAGGGACTTTATGAAGGCCTTTATCCAGTTAAGAAACCCATTG

Alignment

ORF - retro_tbel_4448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.46 %
• Parental protein coverage: 68.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VERIVDKRKNKKGKWEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEFNGLHVSKDKRIRPGKQSNTSKLL
          .E.IVDK.........YL.RWKGYGSTEDTWEPEHHLLHCEEFID.F.GLHVSKDKRIRPGKQSNTSKLL
Retrocopy IEKIVDKXXXXXXX*KYLTRWKGYGSTEDTWEPEHHLLHCEEFID*FHGLHVSKDKRIRPGKQSNTSKLL

Parental  RDSRSPASEKLAHRPSEPGKSKGTSHKRKRINPPLSKPKKGYSGKPPTGGDRAAKTVSYRTTPSGLQIMP
          RDSRS..SEKLAHRPSEPGKSKGTSHK.K.INPPLSK.KKGYS.KPP.GG.RAAK.VSYRTTPSGL.IMP
Retrocopy RDSRSSPSEKLAHRPSEPGKSKGTSHKWKCINPPLSKRKKGYSSKPPAGGNRAAKMVSYRTTPSGLKIMP

Parental  LKR-QNGMENGDA-SEKDERHFGNGSHQPGLDLNDHVGEQDVGDCEVNHAALAENGLGSALTNGGLNLHS
          LK..QNGMEN.D..SEKDERHFGNGSHQPGLDL.DHVGEQDV.DCEVNHAALAENGLGSALTNG.LN.HS
Retrocopy LKKAQNGMENRDTGSEKDERHFGNGSHQPGLDLKDHVGEQDVDDCEVNHAALAENGLGSALTNGVLNFHS

Parental  PVKRKLETEKDYVFDKRLRYSVRQNESNCRFRDIVVRKEEGFTHILLSSQTSDNNALXXXIMKEVRRALC
          P.KRKLETEKDYVFDKRLRYS..QNESNCRF..IVV.KEEG.THILLSSQTSDNNAL...IMKEVRRALC
Retrocopy PAKRKLETEKDYVFDKRLRYSICQNESNCRFQNIVVQKEEGVTHILLSSQTSDNNALTPEIMKEVRRALC

Parental  NAATDDSKLLLLSAVGSVFCSGLDYSYLIGRLSSDRRKESTRIAEAIRDFVKAFIQFKKPI
          NAATDDSKLLL.SAVG.VF.SGLDYS.LIG.LSSDRRKESTRIAEAIRDF.KAFIQ...P.
Retrocopy NAATDDSKLLLFSAVGTVFWSGLDYSNLIGQLSSDRRKESTRIAEAIRDFMKAFIQLRNPL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_4448 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4448 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000000034	5 retrocopies	retro_tbel_1040, retro_tbel_3676, retro_tbel_4160, retro_tbel_4448 , retro_tbel_4710,
Tupaia belangeri	ENSTBEG00000008062	1 retrocopy	retro_tbel_4165,
Tupaia belangeri	ENSTBEG00000015862	2 retrocopies	retro_tbel_2398, retro_tbel_814,